Phylogenomics Yields New Insight Into Relationships Within Vernonieae (Asteraceae)

被引:30
作者
Siniscalchi, Carolina M. [1 ,2 ]
Loeuille, Benoit [3 ]
Funk, Vicki A. [4 ]
Mandel, Jennifer R. [1 ]
Pirani, Jose R. [2 ]
机构
[1] Univ Memphis, Dept Biol Sci, Mandel Lab, Memphis, TN 38152 USA
[2] Univ Sao Paulo, Inst Biociencias, Dept Bot, Lab Sistemat Vegetal, Sao Paulo, SP, Brazil
[3] Univ Fed Pernambuco, Dept Bot CCB, Recife, PE, Brazil
[4] Smithsonian Inst, Natl Museum Nat Hist, Dept Bot, Washington, DC 20560 USA
来源
FRONTIERS IN PLANT SCIENCE | 2019年 / 10卷
基金
美国国家科学基金会;
关键词
Compositae; Hyb-Seq; phylogeny; target capture; Vernonia; PHYLOGENETIC ANALYSIS; POLLEN MORPHOLOGY; MISSING DATA; COMPOSITAE; TAXA; LYCHNOPHORINAE; ALGORITHM; EVOLUTION; THOUSANDS; SYNOPSIS;
D O I
10.3389/fpls.2019.01224
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
Asteraceae, or the sunflower family, is the largest family of flowering plants and is usually considered difficult to work with, not only due to its size, but also because of the abundant cases of polyploidy and ancient whole-genome duplications. Traditional molecular systematics studies were often impaired by the low levels of variation found in chloroplast markers and the high paralogy of traditional nuclear markers like ITS. Next-generation sequencing and novel phylogenomics methods, such as target capture and Hyb-Seq, have provided new ways of studying the phylogeny of the family with great success. While the resolution of the backbone of the family is in progress with some results already published, smaller studies focusing on internal clades of the phylogeny are important to increase sampling and allow morphological, biogeography, and diversification analyses, as well as serving as basis to test the current infrafamilial classification. Vernonieae is one of the largest tribes in the family, accounting for approximately 1,500 species. From the 1970s to the 1990s, the tribe went through several reappraisals, mainly due to the splitting of the mega genus Vernonia into several smaller segregates. Only three phylogenetic studies focusing on the Vernonieae have been published to date, both using a few molecular markers, overall presenting low resolution and support in deepest nodes, and presenting conflicting topologies when compared. In this study, we present the first attempt at studying the phylogeny of Vernonieae using phylogenomics. Even though our sampling includes only around 4% of the diversity of the tribe, we achieved complete resolution of the phylogeny with high support recovering approximately 700 nuclear markers obtained through target capture. We also analyzed the effect of missing data using two different matrices with different number of markers and the difference between concatenated and gene tree analysis.
引用
收藏
页数:16
相关论文
共 66 条
[11]  
Candolle A. P, 1836, PRODROMUS SYSTEMATIS, V5, P9
[12]   TARGETED ENRICHMENT STRATEGIES FOR NEXT-GENERATION PLANT BIOLOGY [J].
Cronn, Richard ;
Knaus, Brian J. ;
Liston, Aaron ;
Maughan, Peter J. ;
Parks, Matthew ;
Syring, John V. ;
Udall, Joshua .
AMERICAN JOURNAL OF BOTANY, 2012, 99 (02) :291-311
[13]   jModelTest 2: more models, new heuristics and parallel computing [J].
Darriba, Diego ;
Taboada, Guillermo L. ;
Doallo, Ramon ;
Posada, David .
NATURE METHODS, 2012, 9 (08) :772-772
[14]   Allocephalus gamolepis, a New Genus and Species of Dipterocypselinae (Vernonieae, Asteraceae) from Central Brazil [J].
de Azevedo Bringel, Joao Bernardo, Jr. ;
Nakajima, Jimi Naoki ;
Robinson, Harold .
SYSTEMATIC BOTANY, 2011, 36 (03) :785-788
[15]  
Dillon M O., 2009, Systematics, Evolution, and Biogeography of Compositae, P417
[16]   THE IMPORTANCE OF FOSSILS IN PHYLOGENY RECONSTRUCTION [J].
DONOGHUE, MJ ;
DOYLE, JA ;
GAUTHIER, J ;
KLUGE, AG ;
ROWE, T .
ANNUAL REVIEW OF ECOLOGY AND SYSTEMATICS, 1989, 20 :431-460
[17]   Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics [J].
Edwards, Scott V. ;
Xi, Zhenxiang ;
Janke, Axel ;
Faircloth, Brant C. ;
McCormack, John E. ;
Glenn, Travis C. ;
Zhong, Bojian ;
Wu, Shaoyuan ;
Lemmon, Emily Moriarty ;
Lemmon, Alan R. ;
Leache, Adam D. ;
Liu, Liang ;
Davis, Charles C. .
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2016, 94 :447-462
[18]   PHYLUCE is a software package for the analysis of conserved genomic loci [J].
Faircloth, Brant C. .
BIOINFORMATICS, 2016, 32 (05) :786-788
[19]   Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales [J].
Faircloth, Brant C. ;
McCormack, John E. ;
Crawford, Nicholas G. ;
Harvey, Michael G. ;
Brumfield, Robb T. ;
Glenn, Travis C. .
SYSTEMATIC BIOLOGY, 2012, 61 (05) :717-726
[20]   A PROTOCOL FOR TARGETED ENRICHMENT OF INTRON-CONTAINING SEQUENCE MARKERS FOR RECENT RADIATIONS: A PHYLOGENOMIC EXAMPLE FROM HEUCHERA (SAXIFRAGACEAE) [J].
Folk, Ryan A. ;
Mandel, Jennifer R. ;
Freudenstein, John V. .
APPLICATIONS IN PLANT SCIENCES, 2015, 3 (08)